The synthesis of the glycosylphosphatidylinositol (GPI) anchor occurs in different compartments within the ER. We have previously shown that GPI anchor intermediates including GlcNAc-PI and GlcN-(acyl)PI are present in Triton insoluble membranes (TIMs), believed to be derived from lipid rafts. The present study was initiated to determine if GPI anchor intermediates move to raft-like domains after their synthesis or if these domains represent another ER compartment for GPI anchor synthesis. We determined that in transfected cells Pig-Ap and Pig-Lp, two proteins involved in the synthesis of GlcNAc-PI and GlcN-PI, respectively, are present in TIMs. In addition, we detected GlcNAc-PI synthase, GlcNAc-PI deacetylase, and GlcN-PI acyltransferase activities in TIMs isolated from untransfected cells. These results lend support to the possibility of additional GPI biosynthetic compartments in the ER and to the notion that GPI anchor intermediates produced in and outside raft-like domains may have a different fate.